control substitution on

statement ok
CREATE EXTERNAL TABLE gff_table STORED AS GFF OPTIONS (file_extension '.gff3') LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/gff/test.gff3';

query T
SELECT seqname, source, start, "end", score, strand, phase FROM gff_table LIMIT 1;
----
sq0 caat 8 13 NULL + NULL

statement ok
DROP TABLE gff_table;

statement ok
CREATE EXTERNAL TABLE gff_table STORED AS GFF OPTIONS (file_extension '.gff3', compression gzip) LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/gff/test.gff3.gz';

query T
SELECT seqname, source, start, "end", score, strand, phase FROM gff_table LIMIT 1;
----
sq0 caat 8 13 NULL + NULL

statement ok
DROP TABLE gff_table;

statement ok
CREATE EXTERNAL TABLE gff_table STORED AS GFF LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/gff/test.gff';

query T
SELECT seqname, source, start, "end", score, strand, phase FROM gff_table LIMIT 1;
----
sq0 caat 8 13 NULL + NULL

statement ok
DROP TABLE gff_table;

statement ok
CREATE EXTERNAL TABLE gff_table STORED AS GFF LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/gff/test.gff.gz' OPTIONS (compression gzip);

query T
SELECT seqname, source, start, "end", score, strand, phase FROM gff_table LIMIT 1;
----
sq0 caat 8 13 NULL + NULL

statement ok
DROP TABLE gff_table;

statement ok
CREATE EXTERNAL TABLE gff_table STORED AS GFF LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/gff/test.gff.zst' OPTIONS (compression zstd);

query T
SELECT seqname, source, start, "end", score, strand, phase FROM gff_table LIMIT 1;
----
sq0 caat 8 13 NULL + NULL

statement ok
DROP TABLE gff_table;

statement ok
CREATE EXTERNAL TABLE gff_table STORED AS GFF PARTITIONED BY (sample) LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/gff-partition/';

query T
SELECT seqname, sample FROM gff_table WHERE sample = '1' LIMIT 1;
----
sq0 1

query T
SELECT COUNT(*) FROM gff_table WHERE sample = '1';
----
5000

query T
SELECT COUNT(*) FROM gff_table;
----
10000

statement ok
DROP TABLE gff_table;

query T
SELECT COUNT(*) FROM gff_scan('$CARGO_MANIFEST_DIR/test-data/datasources/gff/test.gff');
----
5000

query T
SELECT COUNT(*) FROM gff_scan('$CARGO_MANIFEST_DIR/test-data/datasources/gff-partition/');
----
10000

query T
SELECT COUNT(*) FROM gff_scan('$CARGO_MANIFEST_DIR/test-data/datasources/gff/test.gff.gz', 'gzip');
----
5000

query T
SELECT COUNT(*) FROM gff_indexed_scan('$CARGO_MANIFEST_DIR/test-data/datasources/gff-index/gencode.v38.polyAs.gff.gz', 'chr1');
----
8786

query T
SELECT COUNT(*) FROM gff_indexed_scan('$CARGO_MANIFEST_DIR/test-data/datasources/gff-index/gencode.v38.polyAs.gff.gz', 'chr2');
----
7091

statement ok
CREATE EXTERNAL TABLE new_gff STORED AS INDEXED_GFF OPTIONS (compression gzip) LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/gff-index';

query T
SELECT COUNT(*) AS cnt FROM new_gff WHERE gff_region_filter('chr1', seqname) = true
----
8786

statement ok
DROP TABLE new_gff;

query T
COPY (SELECT * FROM gff_scan('$CARGO_MANIFEST_DIR/test-data/datasources/gff-prod/ecoli.gff')) TO '/tmp/test.parquet';
----
7